Run Molscrub as a Python .EXE file

scripts/scrub.py → scrubber/main.py

@@ -377,7 +377,7 @@ def scrub_and_debug(input_mol, _=None):
     isomer_list = scrub(input_mol)
     return (isomer_list, log)
 
-def write_and_log(isomer_list, log, counter):
+def write_and_log(isomer_list, log, counter, w):
     counter["supplied"] += 1
     if log["input_mol_none"]:
         counter["rdkit_nope"] += 1
@@ -417,20 +417,20 @@ def write_and_log(isomer_list, log, counter):
     scrub_fn = scrub_and_catch_errors
     sdwriter_failures = None
 
-if __name__ == '__main__':
+def main():
     with Writer(args.out_fname) as w:
         if args.cpu == 1:
             for input_mol in supplier:
                 isomer_list, log = scrub_fn(input_mol, sdwriter_failures)
-                write_and_log(isomer_list, log, counter)
+                write_and_log(isomer_list, log, counter, w)
         else:
             if args.cpu < 1:
                 nr_proc = multiprocessing.cpu_count()
             else:
                 nr_proc = args.cpu
             p = multiprocessing.Pool(nr_proc - 1) # leave 1 for main process
             for (isomer_list, log) in p.imap_unordered(scrub_fn, supplier):
-                write_and_log(isomer_list, log, counter)
+                write_and_log(isomer_list, log, counter, w)
 
 
     if sdwriter_failures is not None:
@@ -445,3 +445,6 @@ def write_and_log(isomer_list, log, counter):
         with open(fname, "w") as f:
             json.dump(supplier.names, f)
         print("Done.")
+
+if __name__ == '__main__':
+    main()

setup.py

@@ -1,41 +1,33 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-
-import os
-import fnmatch
 from setuptools import setup, find_packages
 
-
-# Path to the directory that contains this setup.py file.
-base_dir = os.path.abspath(os.path.dirname(__file__))
-
-
-def find_files(directory):
-    matches = []
-    for root, dirnames, filenames in os.walk(directory):
-        for filename in fnmatch.filter(filenames, "*"):
-            matches.append(os.path.join(root, filename))
-    return matches
-
+with open("README.md") as file:
+    readme = file.read()
 
 setup(
     name="molscrub",
     author="Forli Lab",
     version="0.1.1",
+    license="GPL-v3",
     author_email="forli@scripps.edu",
     url="https://github.com/forlilab/molscrub",
     description="Enumerate states of small organic molecules: 3D coordinates, tautomers, pH-based adjustments",
-    long_description=open(os.path.join(base_dir, "README.md")).read(),
+    long_description=readme,
     long_description_content_type="text/markdown",
     packages=find_packages(),
-    scripts=[
-        "scripts/scrub.py",
-    ],
-    package_data={"scrubber": ["data/*"]},
-    data_files=[("", ["README.md", "LICENSE"]), ("scripts", find_files("scripts"))],
+    entry_points={
+        'console_scripts': [
+            'scrub.py=scrubber.main:main',
+        ]
+    },
+    package_data={
+        "scrubber": ["data/*"]
+    },
     include_package_data=True,
-    zip_safe=False,
-    install_requires=["rdkit>=2022.03.1"],
+    zip_safe=True,
+    install_requires=[
+        "rdkit>=2022.03.1"
+    ],
     python_requires=">=3.8",
-    license="GPL-v3",
-)
+)